data_3CLV # _model_server_result.job_id LABTCAWF_v1GnbmtKk3sQA _model_server_result.datetime_utc '2024-11-26 01:31:16' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3clv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":211}' # _entry.id 3CLV # _exptl.entry_id 3CLV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3CLV _cell.length_a 66.964 _cell.length_b 66.964 _cell.length_c 76.128 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 25.376 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 3CLV _atom_sites.fract_transf_matrix[1][1] 0.014933 _atom_sites.fract_transf_matrix[1][2] 0.008622 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017244 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013136 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CL A 1 209 1 CL CL . C 2 CL A 1 210 2 CL CL . D 3 GDP A 1 211 1 GDP GDP . E 4 HOH A 1 212 1 HOH HOH . E 4 HOH A 2 213 2 HOH HOH . E 4 HOH A 3 214 3 HOH HOH . E 4 HOH A 4 215 4 HOH HOH . E 4 HOH A 5 216 5 HOH HOH . E 4 HOH A 6 217 6 HOH HOH . E 4 HOH A 7 218 7 HOH HOH . E 4 HOH A 8 219 8 HOH HOH . E 4 HOH A 9 220 9 HOH HOH . E 4 HOH A 10 221 10 HOH HOH . E 4 HOH A 11 222 11 HOH HOH . E 4 HOH A 12 223 12 HOH HOH . E 4 HOH A 13 224 13 HOH HOH . E 4 HOH A 14 225 14 HOH HOH . E 4 HOH A 15 226 15 HOH HOH . E 4 HOH A 16 227 16 HOH HOH . E 4 HOH A 17 228 17 HOH HOH . E 4 HOH A 18 229 18 HOH HOH . E 4 HOH A 19 230 19 HOH HOH . E 4 HOH A 20 231 20 HOH HOH . E 4 HOH A 21 232 21 HOH HOH . E 4 HOH A 22 233 22 HOH HOH . E 4 HOH A 23 234 23 HOH HOH . E 4 HOH A 24 235 24 HOH HOH . E 4 HOH A 25 236 25 HOH HOH . E 4 HOH A 26 237 26 HOH HOH . E 4 HOH A 27 238 27 HOH HOH . E 4 HOH A 28 239 28 HOH HOH . E 4 HOH A 29 240 29 HOH HOH . E 4 HOH A 30 241 2 HOH HOH . E 4 HOH A 31 242 3 HOH HOH . E 4 HOH A 32 243 4 HOH HOH . E 4 HOH A 33 244 5 HOH HOH . E 4 HOH A 34 245 6 HOH HOH . E 4 HOH A 35 246 7 HOH HOH . E 4 HOH A 36 247 8 HOH HOH . E 4 HOH A 37 248 9 HOH HOH . E 4 HOH A 38 249 10 HOH HOH . E 4 HOH A 39 250 11 HOH HOH . E 4 HOH A 40 251 12 HOH HOH . E 4 HOH A 41 252 13 HOH HOH . E 4 HOH A 42 253 14 HOH HOH . E 4 HOH A 43 254 15 HOH HOH . E 4 HOH A 44 255 16 HOH HOH . E 4 HOH A 45 256 17 HOH HOH . E 4 HOH A 46 257 18 HOH HOH . E 4 HOH A 47 258 19 HOH HOH . E 4 HOH A 48 259 20 HOH HOH . E 4 HOH A 49 260 21 HOH HOH . E 4 HOH A 50 261 22 HOH HOH . E 4 HOH A 51 262 23 HOH HOH . E 4 HOH A 52 263 25 HOH HOH . E 4 HOH A 53 264 26 HOH HOH . E 4 HOH A 54 265 27 HOH HOH . E 4 HOH A 55 266 28 HOH HOH . E 4 HOH A 56 267 31 HOH HOH . E 4 HOH A 57 268 32 HOH HOH . E 4 HOH A 58 269 33 HOH HOH . E 4 HOH A 59 270 34 HOH HOH . E 4 HOH A 60 271 35 HOH HOH . E 4 HOH A 61 272 37 HOH HOH . E 4 HOH A 62 273 38 HOH HOH . E 4 HOH A 63 274 39 HOH HOH . E 4 HOH A 64 275 42 HOH HOH . E 4 HOH A 65 276 43 HOH HOH . E 4 HOH A 66 277 45 HOH HOH . E 4 HOH A 67 278 46 HOH HOH . E 4 HOH A 68 279 48 HOH HOH . E 4 HOH A 69 280 49 HOH HOH . E 4 HOH A 70 281 52 HOH HOH . E 4 HOH A 71 282 53 HOH HOH . E 4 HOH A 72 283 54 HOH HOH . E 4 HOH A 73 284 56 HOH HOH . E 4 HOH A 74 285 57 HOH HOH . E 4 HOH A 75 286 58 HOH HOH . E 4 HOH A 76 287 59 HOH HOH . E 4 HOH A 77 288 60 HOH HOH . E 4 HOH A 78 289 62 HOH HOH . E 4 HOH A 79 290 63 HOH HOH . E 4 HOH A 80 291 64 HOH HOH . E 4 HOH A 81 292 65 HOH HOH . E 4 HOH A 82 293 66 HOH HOH . E 4 HOH A 83 294 72 HOH HOH . E 4 HOH A 84 295 73 HOH HOH . E 4 HOH A 85 296 78 HOH HOH . E 4 HOH A 86 297 80 HOH HOH . E 4 HOH A 87 298 81 HOH HOH . E 4 HOH A 88 299 82 HOH HOH . E 4 HOH A 89 300 84 HOH HOH . E 4 HOH A 90 301 86 HOH HOH . E 4 HOH A 91 302 87 HOH HOH . E 4 HOH A 92 303 89 HOH HOH . E 4 HOH A 93 304 90 HOH HOH . E 4 HOH A 94 305 91 HOH HOH . E 4 HOH A 95 306 93 HOH HOH . E 4 HOH A 96 307 2 HOH HOH . E 4 HOH A 97 308 4 HOH HOH . E 4 HOH A 98 309 5 HOH HOH . E 4 HOH A 99 310 6 HOH HOH . E 4 HOH A 100 311 8 HOH HOH . E 4 HOH A 101 312 9 HOH HOH . E 4 HOH A 102 313 11 HOH HOH . E 4 HOH A 103 314 12 HOH HOH . E 4 HOH A 104 315 13 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . . . D 3 -41.461 -2.339 -4.524 1 13.92 ? PB GDP 211 A 1 HETATM 2 O O1B GDP . . . D 3 -40.697 -3.32 -3.695 1 13.89 ? O1B GDP 211 A 1 HETATM 3 O O2B GDP . . . D 3 -42.84 -2.105 -3.95 1 15.06 ? O2B GDP 211 A 1 HETATM 4 O O3B GDP . . . D 3 -40.763 -1.009 -4.654 1 16.6 ? O3B GDP 211 A 1 HETATM 5 O O3A GDP . . . D 3 -41.624 -2.873 -6.047 1 14.52 ? O3A GDP 211 A 1 HETATM 6 P PA GDP . . . D 3 -41.643 -4.428 -6.516 1 14.47 ? PA GDP 211 A 1 HETATM 7 O O1A GDP . . . D 3 -42.694 -5.202 -5.737 1 14.84 ? O1A GDP 211 A 1 HETATM 8 O O2A GDP . . . D 3 -40.286 -5.06 -6.536 1 15.27 ? O2A GDP 211 A 1 HETATM 9 O O5' GDP . . . D 3 -42.165 -4.272 -8.029 1 16.04 ? O5' GDP 211 A 1 HETATM 10 C C5' GDP . . . D 3 -43.455 -3.733 -8.341 1 14.39 ? C5' GDP 211 A 1 HETATM 11 C C4' GDP . . . D 3 -43.841 -4.211 -9.746 1 16 ? C4' GDP 211 A 1 HETATM 12 O O4' GDP . . . D 3 -42.976 -3.628 -10.724 1 15.48 ? O4' GDP 211 A 1 HETATM 13 C C3' GDP . . . D 3 -43.761 -5.72 -9.961 1 17.14 ? C3' GDP 211 A 1 HETATM 14 O O3' GDP . . . D 3 -44.853 -6.032 -10.835 1 17.66 ? O3' GDP 211 A 1 HETATM 15 C C2' GDP . . . D 3 -42.442 -5.941 -10.705 1 17.31 ? C2' GDP 211 A 1 HETATM 16 O O2' GDP . . . D 3 -42.427 -7.096 -11.556 1 17.69 ? O2' GDP 211 A 1 HETATM 17 C C1' GDP . . . D 3 -42.363 -4.656 -11.516 1 18.64 ? C1' GDP 211 A 1 HETATM 18 N N9 GDP . . . D 3 -40.978 -4.239 -11.756 1 19.53 ? N9 GDP 211 A 1 HETATM 19 C C8 GDP . . . D 3 -40.019 -4.065 -10.821 1 19.32 ? C8 GDP 211 A 1 HETATM 20 N N7 GDP . . . D 3 -38.87 -3.668 -11.401 1 20.06 ? N7 GDP 211 A 1 HETATM 21 C C5 GDP . . . D 3 -39.103 -3.57 -12.73 1 19.98 ? C5 GDP 211 A 1 HETATM 22 C C6 GDP . . . D 3 -38.318 -3.193 -13.929 1 20.26 ? C6 GDP 211 A 1 HETATM 23 O O6 GDP . . . D 3 -37.116 -2.854 -13.81 1 19.45 ? O6 GDP 211 A 1 HETATM 24 N N1 GDP . . . D 3 -38.946 -3.222 -15.135 1 19.9 ? N1 GDP 211 A 1 HETATM 25 C C2 GDP . . . D 3 -40.25 -3.571 -15.286 1 20.87 ? C2 GDP 211 A 1 HETATM 26 N N2 GDP . . . D 3 -40.792 -3.561 -16.531 1 19.39 ? N2 GDP 211 A 1 HETATM 27 N N3 GDP . . . D 3 -41.033 -3.95 -14.227 1 20.29 ? N3 GDP 211 A 1 HETATM 28 C C4 GDP . . . D 3 -40.508 -3.951 -12.958 1 19.16 ? C4 GDP 211 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #